Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-714.fastq.uq.polyn	RAL-714.filter	percent
uq reads:	38582780	3583346	9.2874%
   reads: 	41002268	3926839	9.5771%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-714.filter	RAL-714.nostrna	percent
uq reads:	3583346	3535055	98.6523%
   reads: 	3926839	3863588	98.3893%
----------------
TE_filter:
  reads:	RAL-714.nostrna	RAL-714.noTE	percent
uq reads:	3535055	3523501	99.6732%
   reads: 	3863588	3849512	99.6357%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-714.noGEN.front	RAL-714.noGEN.front.gen	percent
uq reads:	3523501	1644758	46.6797%
   reads: 	3849512	1812532	47.0847%
----------------
match_TE:2:
  reads:	RAL-714.noGEN.front	RAL-714.noGEN.front.TE	percent
uq reads:	3523501	236976	6.7256%
   reads: 	3849512	241207	6.2659%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-714.noGEN.end	RAL-714.noGEN.end.gen	percent
uq reads:	3523501	589678	16.7356%
   reads: 	3849512	752354	19.5441%
----------------
match_TE:2:
  reads:	RAL-714.noGEN.end	RAL-714.noGEN.end.TE	percent
uq reads:	3523501	117463	3.3337%
   reads: 	3849512	122233	3.1753%
----------------
Candidate insertion sites in file: RAL-714_insert.txt
  reads:	10824
  uqreads:	10644
  Number of Candidate sites:	10644

Level 1 collapse of insertion sites in file: RAL-714_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	589

Level 1 annotation file: RAL-714_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-714_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-714.noGEN.front	RAL-714.noGEN.front.gendel	percent
uq reads:	3523501	1644758	46.6797%
   reads: 	3849512	1812532	47.0847%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-714.noGEN.end	RAL-714.noGEN.end.gendel	percent
uq reads:	3523501	589678	16.7356%
   reads: 	3849512	752354	19.5441%
----------------
Candidate breakpoint sites in file: RAL-714_depletion.xls
  reads:	20904
  uqreads:	20215
  Number of reads supporting candidate sites:	20215

Level 1 collapse of depletion sites in file: RAL-714_depletion_level1.xls
  Number of Level 1 collapsed sites:	1934